Sys.time()
## [1] "2015-03-19 13:09:27 SAST"
print(prefix)
## [1] "CCAGCTGGTTATGCGATTCTMARGTG"
print(suffix)
## [1] "CTGAGCGTGTGGCAAGGCCC"
print(motif_length)
## [1] 9
n_matched <- length(motif_dat$matched_seq)
n_unmatched <- length(motif_dat$unmatched_seq)
n_total <- n_matched + n_unmatched
kable(data.frame(seq_matched_count = n_matched,
seq_matched_perc = 100*round(n_matched / n_total, 4),
seq_unmatched_count = n_unmatched,
seq_unmatched_perc = 100*round(n_unmatched / n_total, 4)))
| seq_matched_count| seq_matched_perc| seq_unmatched_count| seq_unmatched_perc| |-----------------:|----------------:|-------------------:|------------------:| | 11561| 79.32| 3014| 20.68|
print(motif_dat$matched_seq)
## A DNAStringSet instance of length 11561
## width seq names
## [1] 299 TATGGGATCAAAGTCTAAA...CCTATACATTATTGTGCT CTTACCTAA
## [2] 299 TATGGGACGAAAGCCTCAA...CCTATACATTATTGTGCT TTAGATGTT
## [3] 308 TATGGGACGAAAGTCTAAA...CCTATACATTATTGTGCT TATTGGGGC
## [4] 299 TATGGGACGAAAGCCTCAA...CCTATACATTATTGTGCT ATTGTGCCA
## [5] 299 TATGGGATGAAAGCCTCAA...CCTATACATTATTGTGCT GTAGACTGT
## ... ... ...
## [11557] 299 TATGGGACGAAAGTCTAAA...CCTATACATTATTGTGCT GTACACAAG
## [11558] 299 TATGGGACGAAAGCCTCAA...CCTATACATTATTGTGCT CATTTAAAA
## [11559] 299 TATGGGACGAAAGTCTCAA...CCTATACATTATTGTGCT GCTCAAGTA
## [11560] 308 TATGGGATCAAAGTCTAAA...CCTATACATTATTGTGCT AATCCTCTA
## [11561] 299 TATGGGACGAAAGTCTAAA...CCTATACATTATGGTGCT TAATTGCGA
Counts of the letters in the matched sequences.
x <- apply(consensusMatrix(motif_dat$matched_seq), 1, sum)
x <- x[x != 0]
kable(data.frame(letter = names(x),
count = x,
count_per_seq = round(x/length(motif_dat$matched_seq),2),
row.names = 1:length(x)))
|letter | count| count_per_seq| |:------|-------:|-------------:| |A | 1296178| 112.12| |C | 675110| 58.40| |G | 536220| 46.38| |T | 978310| 84.62| |+ | 2| 0.00|
Normalized counts of the letters in the matched sequences.
x_freq <- round(x/sum(x), 4)
kable(data.frame(letter = names(x_freq),
count = x_freq,
row.names = 1:length(x_freq)))
|letter | count| |:------|------:| |A | 0.3718| |C | 0.1937| |G | 0.1538| |T | 0.2807| |+ | 0.0000|
barplot(x/sum(x),
main = 'Normalized counts of the letters\nin the matched sequences')
hist(width(motif_dat$matched_seq),
main = "Histogram of the lengths of the matched sequences",
xlab = "Sequence Length",
ylab = "Number of Sequences")
print(motif_dat$unmatched_seq)
## A DNAStringSet instance of length 3014
## width seq names
## [1] 419 AATGTCAGCACAGTACAAT...CCTGAGCGTGTGGCAAGGC seq_4
## [2] 351 TATGGGACCAAAGTCTAAA...ACTGAGCGTGTGGCAAGGC seq_5
## [3] 353 TATGGGACGAAAGCCTCAA...CCTGAGCGTGTGGCAAGGC seq_10
## [4] 351 TATGGGACGAAAGCCTCAA...CCTGAGCGTGTGGCAAGGC seq_15
## [5] 343 TATGGGATGAAAGCCTAAA...CCTGAGCGTGTGGCAAGGC seq_17
## ... ... ...
## [3010] 419 AATGTCAGTACAGTACAAT...ACTGAGCGTGTGGCAAGGC seq_14561
## [3011] 419 AATGTCAGTACAGTACAAT...ACTGAGCGTGTGGCAAGGC seq_14562
## [3012] 418 AATGTCAGTACAGTACAAT...CCTGAGCGTGTGGCAAGGC seq_14563
## [3013] 419 AATGTAAGCACAGTACAAT...CCTGAGCGTGTGGCAAGGC seq_14564
## [3014] 419 AATGTCAGTACAGTACAAT...GCTGAGCTTGTGGCAAGGC seq_14566
Counts of the letters in the unmatched sequences.
x <- apply(consensusMatrix(motif_dat$unmatched_seq), 1, sum)
x <- x[x != 0]
kable(data.frame(letter = names(x),
count = x,
count_per_seq = round(x/length(motif_dat$unmatched_seq),2),
row.names = 1:length(x)))
|letter | count| count_per_seq| |:------|------:|-------------:| |A | 466241| 154.69| |C | 213997| 71.00| |G | 241376| 80.08| |T | 266341| 88.37| |+ | 8| 0.00|
Normalized counts of the letters in the unmatched sequences.
x_freq <- round(x/sum(x), 4)
kable(data.frame(letter = names(x_freq),
count = x_freq,
row.names = 1:length(x_freq)))
|letter | count| |:------|------:| |A | 0.3925| |C | 0.1801| |G | 0.2032| |T | 0.2242| |+ | 0.0000|
barplot(x/sum(x),
main = 'Normalized counts of the letters\nin the unmatched sequences')
hist(width(motif_dat$unmatched_seq),
main = "Histogram of the lengths of the unmatched sequences",
xlab = "Sequence Length",
ylab = "Number of Sequences")
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